EMDB Validation Analysis : EMD-0132

EMD-0132 › Validation analysis

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Cryo-EM structure of the BRISC complex bound to SHMT2

Validation summary

Resolution:
Method:
Map released:
Last modified:
Sample name:
3.9 Å (depositor provided) (FSC 0.143 CUT-OFF)
Single particle reconstruction
2019-07-10
2020-11-25
BRISC complex bound to SHMT2 alpha
Organism:
Fitted atomic model:
Homo sapiens
6h3c (10 chains, 12406 atoms)

Model evaluation bars:

Model Metric Evaluation bar Average value
6h3c Q-score
0.278
Atom Inclusion
0.773
CCC
0.619
SMOC
0.728

Additional validation information

Please find validation analyses used for peer review in the wwPDB validation reports for this entries map (EMD-0132) and model-map (6h3c and EMD-0132). Validation analysis of this entry is available in the main page. Documentation for the outputs of EMDB Validation Analysis can be found on the help page.

Map parameters

Recommended contour level:
Number of grid points:
Voxel size:
Minimum value:
Maximum value:
Average value:
Standard deviation:
0.00816
350 × 350 × 350
0.860 × 0.860 × 0.860 Å
-0.066
0.131
0.000
0.003
Image not available

Primary map visualisation

Projections

Raw map visualisation (Raw map calculated from deposited two half-maps)

Volume graphs
Download: EMDB Mask Learn more EMDB Raw Map Learn more Depositor Half Map 1 Depositor Half Map 2
Map resolution (Å) measured by Fourier Shell Correlation (FSC)
EMDB calculated FSC Author FSC
Threshold Unmasked Masked Corrected Author
FSC 0.143 4.36 3.90 3.90 3.81
FSC 0.5 7.10 4.45 4.45 4.38
FSC half-bit 4.42 4.01 4.00 3.84

Map and 1 fitted model

Map with model 6h3c (Cryo-EM structure of the BRISC complex bound to SHMT2)
Primary map with model views
Title
X projection

X

Y projection

Y

Z projection

Z

Map-model fit plots
Chain scores summary
Strudel Information
Chain:
Score range:

Depositor mask(s)

Mask with primary map (msk_1)
Title
X projection

X

Y projection

Y

Z projection

Z

EMDB generated mask(s)

FSC mask with raw map
Title
X projection

X

Y projection

Y

Z projection

Z

Symmetry Information
  • Symmetry table (Applied symmetry: C2)
    • Symmetry type Symmetry fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees) Peak height
      Symmetry axis #1 C 2 -0.007961, -0.006196, +0.9999 +180 +0.9762
  • Symmetry element table
    • Symmetry element type Symmetry element fold Directional vector of symmetry axis
      X, Y, Z      		 Angle (degrees)
      Symmetry element #1 E +1 +1, +0, +0 +0
      Symmetry element #2 C +2 -0.007961, -0.006196, +0.9999 +180